12 bits tif image issue with skimage 0.5dev

[jip]

Hi,
Thank you for your explanations.
Jean-Patrick

On 9 déc, 17:12, Christoph Gohlke <cjgoh... at gmail.com> wrote:
> On 12/9/2011 2:47 AM, jip wrote:
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> > Dear all,
> > I update skimage to 0.5 dev on my ubuntu box. ipython startup gives:
> > Imported NumPy 1.3.0, SciPy 0.7.2, Matplotlib 0.99.3 + guidata 1.2.5,
> > guiqwt 2.0.8.1
> > Type "scientific" for more details.
> > >>> import skimage
> > >>> skimage.version
> > <module 'skimage.version' from
> > '/usr/local/lib/python2.6/dist-packages/scikits_image-0.5dev-py2.6-linux-i686.egg/skimage/version.pyc'>
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> > A 12 bits tif image when loaded with skimage do not behave like the
> > same image loaded with an other library (readmagick, mahotas), as
> > shown above. When a 8 bits png image is loaded, the differences
> > (orientation, saturation) vanish.
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> > In a previous message Neil Yager said thatthe issue was fixed
> > <https://groups.google.com/forum/#%21topic/scikits-image/JSvqMzOgTEE>.
> > What should I do to fix the problem on my machine?
> > Thank you.
>
> > Jean-Patrick
>
> Hi,
>
> the PIL plugin has been fixed to correctly read 16 bit images. A PR for
> imshow is pending. The matplotlib plugin, which internally also uses
> PIL, is still broken. Matplotlib returns 8 bit, flipped images (by
> design it seems).
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> The problem is that PIL does not handle 16 bit images well. The solution
> in this case is to use more capable plugins for reading (e.g. FreeImage)
> and show (matplotlib ):
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> skimage.io.use_plugin('matplotlib', 'imshow')
> skimage.io.use_plugin('freeimage', 'imread')
>
> Christoph